DNA-DNA Homology, Murein Types and Enzyme Patterns in the Type Strains of the Genus Bifidobacterium

Deoxyribonucleic acid (DNA) homology among 10 strains of spiroplasma associated with plants and insects was assessed by analysis of DNA–DNA hybrids with single strand specific S1 nuclease. Based on DNA homology, the spiroplasmas could be divided into three genetically distinct groups (designated I, II, and III), corresponding to three separate serogroups described previously. DNA sequence homology between the three groups was ≤5%. Based on DNA homology, group I could be divided into three subgroups (A, B, and C) that corresponded to three serological subgroups of serogroup I. Subgroup A contained Spiroplasma citri strains Maroc R8A2 and C 189; subgroup B contained strains AS 576 from honey bee and G 1 from flowers; subgroup C contained corn stunt spiroplasma strains 1-747 and PU 8-17. There was 27–54% DNA sequence homology among these three subgroups. Group II contained strains 23-6 and 27-31 isolated from flowers of tulip tree (Liriodendron tulipifera L.). Group III contained strains SR 3 and SR 9, other isolates from flowers of tulip tree. Based on thermal denaturation, guanine plus cytosine contents of DNA from five type strains representing all groups and subgroups were estimated to be close to 26 mol% for group I strains, close to 25 mol% for group II strains, and close to 29 mol% for group III strains. The genome molecular weights of these five type strains were all estimated to be about 109.

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Ruthenium red and alcian blue effects on outer structures of methanotrophic bacteria

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102444 ◽

1988 ◽

Vol 46 ◽

pp. 72-73

Author(s):

T.A. Fassel ◽

M.J. Schaller ◽

C.C. Remsen

Keyword(s):

Research Effort ◽

Ruthenium Red ◽

Outer Cell ◽

Methanotrophic Bacteria ◽

En Bloc ◽

Methylosinus Trichosporium ◽

Wall Structures ◽

Methylomonas Albus ◽

Type Strains ◽

Outer Cell Wall

Methane, a contributor to the “greenhouse effect”, is oxidized in the natural environment by methanotrophic bacteria. As part of a comprehensive research effort, we have been examining the ultrastructure of methanotrophs. These microorganisms have complex outer cell wall structures similar to those frequently found in other chemol itho- trophic bacteria. (1,2)In our work, we have focused on the “type” strains of Methylomonas albus BG8 and Methylosinus trichosporium OB3b. Between Spurr and LR White embedding resins, we found a difference 1n the preservation of an outer cup layer of BG8 external to the peripheral membranes. Cells from the same sample embedded in Spurr consistently lacked this feature (FIG. 1). This effect was overcome by an en bloc ruthenium red (RR) protocol that resulted in successful retention of the cup layer in Spurr resin (FIG. 2). For OB3b cells, the en bloc RR protocol resulted in an exterior bead feature distinguishable in thin section (FIG. 4) that previously was seen only by SEM.

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Suitability Analysis of 17 Probiotic Type Strains of Lactic Acid Bacteria as Starter for Kimchi Fermentation

Foods ◽

10.3390/foods10061435 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1435

Author(s):

Hee Seo ◽

Jae-Han Bae ◽

Gayun Kim ◽

Seul-Ah Kim ◽

Byung Hee Ryu ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Growth Rates ◽

Principal Component ◽

Fermented Foods ◽

Suitability Analysis ◽

Moderate Growth ◽

Health Promoting ◽

Highly Correlated ◽

Type Strains

The use of probiotic starters can improve the sensory and health-promoting properties of fermented foods. This study aimed to evaluate the suitability of probiotic lactic acid bacteria (LAB) as a starter for kimchi fermentation. Seventeen probiotic type strains were tested for their growth rates, volatile aroma compounds, metabolites, and sensory characteristics of kimchi, and their characteristics were compared to those of Leuconostoc (Le.) mesenteroides DRC 1506, a commercial kimchi starter. Among the tested strains, Limosilactobacillus fermentum, Limosilactobacillus reuteri, Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and Ligilactobacillus salivarius exhibited high or moderate growth rates in simulated kimchi juice (SKJ) at 37 °C and 15 °C. When these five strains were inoculated in kimchi and metabolite profiles were analyzed during fermentation using GC/MS and 1H-NMR, data from the principal component analysis (PCA) showed that L. fermentum and L. reuteri were highly correlated with Le. mesenteroides in concentrations of sugar, mannitol, lactate, acetate, and total volatile compounds. Sensory test results also indicated that these three strains showed similar sensory preferences. In conclusion, L. fermentum and L. reuteri can be considered potential candidates as probiotic starters or cocultures to develop health-promoting kimchi products.

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A Mutation in a Saccharomyces cerevisiae Gene (RAD3) Required for Nucleotide Excision Repair and Transcription Increases the Efficiency of Mismatch Correction

Genetics ◽

10.1093/genetics/144.2.459 ◽

1996 ◽

Vol 144 (2) ◽

pp. 459-466 ◽

Cited By ~ 1

Author(s):

Yingying Yang ◽

Anthony L Johnson ◽

Leland H Johnston ◽

Wolfram Siede ◽

Errol C Friedberg ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Mismatch Repair ◽

Excision Repair ◽

Spontaneous Mutation ◽

Surprising Result ◽

Spontaneous Mutation Rate ◽

Mismatch Correction ◽

Nucleotide Excision ◽

Repair Genes ◽

Type Strains

Abstract RAD3 functions in DNA repair and transcription in Saccharomyces cerevisiae and particular rad3 alleles confer a mutator phenotype, possibly as a consequence of defective mismatch correction. We assessed the potential involvement of the Rad3 protein in mismatch correction by comparing heteroduplex repair in isogenic rad3-1 and wild-type strains. The rad3-1 allele increased the spontaneous mutation rate but did not prevent heteroduplex repair or bias its directionality. Instead, the efficiency of mismatch correction was enhanced in the rad3-1 strain. This surprising result prompted us to examine expression of yeast mismatch repair genes. We determined that MSH2, but not MLH1, is transcriptionally regulated during the cell-cycle like PMSl, and that rad3-1 does not increase the transcript levels for these genes in log phase cells. These observations suggest that the rad3-1 mutation gives rise to an enhanced efficiency of mismatch correction via a process that does not involve transcriptional regulation of mismatch repair. Interestingly, mismatch repair also was more efficient when error-editing by yeast DNA polymerase δ was eliminated. We discuss our results in relation to possible mechanisms that may link the rad3-1 mutation to mismatch correction efficiency.

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Identification ofvib-1, a Locus Involved in Vegetative Incompatibility Mediated byhet-cinNeurospora crassa

Genetics ◽

10.1093/genetics/162.1.89 ◽

2002 ◽

Vol 162 (1) ◽

pp. 89-101 ◽

Cited By ~ 6

Author(s):

Qijun Xiang ◽

N Louise Glass

Keyword(s):

Acid Phosphatase ◽

Recognition System ◽

Deletion Mutants ◽

Wild Type ◽

Vegetative Incompatibility ◽

Death Rates ◽

Self Recognition ◽

Allelic Differences ◽

Native Gel ◽

Type Strains

AbstractA non-self-recognition system called vegetative incompatibility is ubiquitous in filamentous fungi and is genetically regulated by het loci. Different fungal individuals are unable to form viable heterokaryons if they differ in allelic specificity at a het locus. To identify components of vegetative incompatibility mediated by allelic differences at the het-c locus of Neurospora crassa, we isolated mutants that suppressed phenotypic aspects of het-c vegetative incompatibility. Three deletion mutants were identified; the deletions overlapped each other in an ORF named vib-1 (vegetative incompatibility blocked). Mutations in vib-1 fully relieved growth inhibition and repression of conidiation conferred by het-c vegetative incompatibility and significantly reduced hyphal compartmentation and death rates. The vib-1 mutants displayed a profuse conidiation pattern, suggesting that VIB-1 is a regulator of conidiation. VIB-1 shares a region of similarity to PHOG, a possible phosphate nonrepressible acid phosphatase in Aspergillus nidulans. Native gel analysis of wild-type strains and vib-1 mutants indicated that vib-1 is not the structural gene for nonrepressible acid phosphatase, but rather may regulate nonrepressible acid phosphatase activity.

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Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Veterinary Research ◽

10.1186/s13567-021-00905-1 ◽

2021 ◽

Vol 52 (1) ◽

Author(s):

Jaewon Lim ◽

Hong-Tae Park ◽

Seyoung Ko ◽

Hyun-Eui Park ◽

Gyumin Lee ◽

...

Keyword(s):

Mycobacterium Avium ◽

Phenotypic Diversity ◽

Control Strategies ◽

Genomic Diversity ◽

Phenotypic Traits ◽

Whole Genome ◽

Genomic Features ◽

Phenotypic Differences ◽

Mycobacterium Avium Subsp Paratuberculosis ◽

Type Strains

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

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HET-E and HET-D Belong to a New Subfamily of WD40 Proteins Involved in Vegetative Incompatibility Specificity in the Fungus Podospora anserina

Genetics ◽

10.1093/genetics/161.1.71 ◽

2002 ◽

Vol 161 (1) ◽

pp. 71-81

Author(s):

Eric Espagne ◽

Pascale Balhadère ◽

Marie-Louise Penin ◽

Christian Barreau ◽

Béatrice Turcq

Keyword(s):

Genetic Difference ◽

Podospora Anserina ◽

Wild Type ◽

Incompatible Interaction ◽

Vegetative Incompatibility ◽

Repeat Domain ◽

Upper Face ◽

E1a Gene ◽

Type Strains ◽

Wd40 Repeats

Abstract Vegetative incompatibility, which is very common in filamentous fungi, prevents a viable heterokaryotic cell from being formed by the fusion of filaments from two different wild-type strains. Such incompatibility is always the consequence of at least one genetic difference in specific genes (het genes). In Podospora anserina, alleles of the het-e and het-d loci control heterokaryon viability through genetic interactions with alleles of the unlinked het-c locus. The het-d2Y gene was isolated and shown to have strong similarity with the previously described het-e1A gene. Like the HET-E protein, the HET-D putative protein displayed a GTP-binding domain and seemed to require a minimal number of 11 WD40 repeats to be active in incompatibility. Apart from incompatibility specificity, no other function could be identified by disrupting the het-d gene. Sequence comparison of different het-e alleles suggested that het-e specificity is determined by the sequence of the WD40 repeat domain. In particular, the amino acids present on the upper face of the predicted β-propeller structure defined by this domain may confer the incompatible interaction specificity.

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Indigenous rhizobial strains SEMIA 4108 and SEMIA 4107 for common bean inoculation: A biotechnological tool for cleaner and more sustainable agriculture

Experimental Agriculture ◽

10.1017/s0014479721000041 ◽

2021 ◽

pp. 1-11

Author(s):

Bruno Britto Lisboa ◽

Thomas Müller Schmidt ◽

Arthur Henrique Ely Thomé ◽

Raul Antonio Sperotto ◽

Camila Gazolla Volpiano ◽

...

Keyword(s):

Grain Yield ◽

Common Bean ◽

Field Experiments ◽

Rhizobium Phaseoli ◽

Productivity Losses ◽

Bean Plants ◽

Rrna Sequencing ◽

Low Efficiency ◽

Type Strains ◽

Common Bean Plants

Summary Inoculation of symbiotic N2-fixing rhizobacteria (rhizobia) in legumes is an alternative to reduce synthetic N fertiliser input to crops. Even though common bean benefits from the biological N2 fixation carried out by native rhizobia isolates, the low efficiency of this process highlights the importance of screening new strains for plant inoculation. Two rhizobial strains (SEMIA 4108 and SEMIA 4107) previously showed great potential to improve the growth of common beans under greenhouse conditions. Thus, this study evaluated the growth and grain yield of common bean plants inoculated with those strains in field experiments. The rhizobial identification was performed by 16S rRNA sequencing and the phylogeny showed that SEMIA 4108 and SEMIA 4107 are closely related to Rhizobium phaseoli, within a clade containing other 18 Rhizobium spp. type strains. Common bean plants inoculated with SEMIA 4107 showed similar productivity to N-fertilised (N+) plants in the first experiment (2016/17) and higher productivity in the second experiment (2018/19). The development of inoculated plants was different from that observed for N+. Nonetheless, comparing inoculated treatments with N-fertilised control, no yield or productivity losses at the end of the growing process were detected. Our results showed that inoculation of the rhizobial isolates SEMIA 4108 and SEMIA 4107 improved the growth and grain yield of common bean plants. The observed agronomical performance confirms that both strains were effective and can sustain common bean growth without nitrogen fertilisation under the edaphoclimatic conditions of this study.

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Differences in Liver Folate Enzyme Patterns in Premature and Full Term Infants

Pediatric Research ◽

10.1203/00006450-198208000-00008 ◽

1982 ◽

Vol 16 (8) ◽

pp. 628-631 ◽

Cited By ~ 12

Author(s):

Aida Kalnitsky ◽

David Rosenblatt ◽

Stanley Zlotkin

Keyword(s):

Full Term ◽

Term Infants ◽

Enzyme Patterns ◽

Liver Folate

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Defining the Rhizobium leguminosarum Species Complex

Genes ◽

10.3390/genes12010111 ◽

2021 ◽

Vol 12 (1) ◽

pp. 111 ◽

Cited By ~ 1

Author(s):

J. Peter W. Young ◽

Sara Moeskjær ◽

Alexey Afonin ◽

Praveen Rahi ◽

Marta Maluk ◽

...

Keyword(s):

Ribosomal Rna ◽

Species Complex ◽

Rhizobium Leguminosarum ◽

Housekeeping Genes ◽

Single Species ◽

Natural Unit ◽

Genome Sequences ◽

Distinct Entity ◽

Type Strains ◽

Core Genes

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

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